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I'm not an expert at all in this, so this is just a WAG. Does it have a lockup converter? I would guess when it locks the RPMs would drop about 500 from when it is not locked (at least that's what the drop sounds like when my Neon converter locks up), so maybe the converter has an issue when it goes into lockup. I wouldn't know how to troubleshoot this, but I think you can disable the lockup function by pulling an electrical connection (but I don't know which connection it is), so disabling the lockup and test driving might give you an idea if that's the problem.

Someone should have a little better information on what to do, but I thought I'd throw this out to get the ball rolling...

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I think you hit the nail on the head. Lockup does account for a small drop in RPM when engaged, and can cause shudder when malfunctioning. Lockup is electronically controlled and will be part of a three pin plug on the driver's side of the transmission right behind kick-down lever. Problem with just disconnecting though is overdrive is also incorporated into that plug. The center pin is a common positive between OD and lockup, the front pin is ground switched control for OD, and the back (third) pin is ground switched for lockup. Verify that first though before unplugging things though.